An analysis was performed of the equilibrium binding of a recombination accessory factor, the IHF protein of E. coli to its DNA targets. The results quantitate the degree of specificity for this DNA binding protein and the importance of recognition via the minor groove of DNA. The capacity of a recombinase, the bacteriophage lambda Int protein, to juxtapose potential partners has been established. The bimolecular complex appears to be a synaptic intermediate in the process of site- specific recombination. A new method for trapping recombination intermediates has been devised. The method relies on the properties of an analog of the phosphodiester backbone in which a sulfur replaces a bridging oxygen atom. The phosphorothiolate linkage can be cleaved by Int protein but can not be rejoined. This suicide substrate has been used to demonstrate that the early stages of site-specific recombination do not depend on homology between partners.